Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate 353399 BT3873 asparaginyl-tRNA synthetase (NCBI ptt file)
Query= curated2:Q8TXG4 (431 letters) >FitnessBrowser__Btheta:353399 Length = 467 Score = 180 bits (457), Expect = 7e-50 Identities = 140/450 (31%), Positives = 217/450 (48%), Gaps = 49/450 (10%) Query: 16 GEEVRLAGWVHEVRDLGGIKFVLLRDRTGI--VQLTLPKQKVPKETFEKVPKLTKESVIR 73 G V + GWV R + F+ L D + I VQ+ + +E + + T + I Sbjct: 19 GAMVNVKGWVRTRRGSKQVNFIALNDGSTINNVQIVVDLANFDEEMLKLI---TTGACIS 75 Query: 74 VEGTVQANEKAPGGVEVIPQRIEVLSESDTHLPLDPTGKVDADLDTRLDARVLDLRREEP 133 V G + + + VEV + IEVL D PL G ++ + L R Sbjct: 76 VNGVMVESVGSGQKVEVQAKEIEVLGTCDNTYPLQKKGH---SMEFLREIAHLRPRTNTF 132 Query: 134 QAIFKIRNVVTTAIREFLEERGFIEVHTPKIIASATEGGTELFPVV-------------- 179 A+F+IR+ + AI +F E+GF HTP I S EG ++F V Sbjct: 133 GAVFRIRHNMAIAIHKFFHEKGFFYFHTPIITGSDCEGAGQMFQVTTMNLYDLKKDERGS 192 Query: 180 ------YFERDAYLAQSPQLYKQMLMAAGFERVYEIGPIFRAEEHNTRRHLNEAISVDIE 233 +F + A L S QL + L A +Y GP FRAE NT RHL E ++ E Sbjct: 193 ISYDDDFFGKQASLTVSGQLEGE-LAATALGAIYTFGPTFRAENSNTPRHLAEFWMIEPE 251 Query: 234 MSFIESEEDVMRVLEELLAHVFRKVREECEKELEAL----DRELPE-----LETPFERIT 284 ++F + ++ M + EE + + + + C +++ L D+ L E L+ F R+ Sbjct: 252 VAFNDIADN-MDLAEEFIKYCVKWALDNCADDVKFLNDMFDKGLIERLQGVLKDDFVRLP 310 Query: 285 YEETLDLLSE-----HGIE--VEWGEDLPTEAERKL-GEIFEEPFFITEWPRETRPFYTM 336 Y + + +L + H E V WG DL +E ER L E F+ P +T++P+E + FY Sbjct: 311 YTDGIKILEDAVAKGHKFEFPVYWGVDLASEHERYLVEEHFKRPVILTDYPKEIKAFYMK 370 Query: 337 AKDDEVTT-AFDLMYQGL-ELASGAQREHRYDVLVRQIEEQGLSPEDFRHYLEAFKYGMP 394 +D T A D+++ + E+ G++RE Y+ L+ +IEE + +D YL+ K+G Sbjct: 371 QNEDGKTVRAMDVLFPKIGEIIGGSEREADYNKLMTRIEEMHIPMKDMWWYLDTRKFGTC 430 Query: 395 PHGGWGLGLERTLMTITGAENIREVTLFPR 424 PH G+GLG ER L+ +TG NIR+V FPR Sbjct: 431 PHSGFGLGFERLLLFVTGMSNIRDVIPFPR 460 Lambda K H 0.318 0.138 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 463 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 431 Length of database: 467 Length adjustment: 33 Effective length of query: 398 Effective length of database: 434 Effective search space: 172732 Effective search space used: 172732 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory